Processing Code for Pediatric Airway

Purpose: automatically display the centerline and cross sections,
	 calculate the cross-sectional area for an airway 

Running requirements:
1) Unix/Linux
2) matlab

Prepare:
1) compile code/crossSections
Requirements: 
  -- SlicerExecutionModel/GenerateCLP
  -- ITK
  -- VTK >= 5.10.0

2) Data
  -- Airway binary segmentation: *_Segmented_NoSinuses.nrrd
     generated by the airway segmentation software

  -- Airway geometry: *_Airway_NoSinuses_NoMouth_Smooth.vtk
     generated by the airway segmentation software, sometimes if 
     there is an open mouth, we need to remove it

  -- Landmarks: *_Points.txt
     Right now we use 10 landmarks, 4 of them are used to compute the 
     starting plane for calculating the centerline, 5 are used in the
     landmark-based registration, 1, the subglottic, are used in the 
     airway measurement     

  -- Remove mouth: *_CuttingPlanes.txt
     produced when removing the mouth from the above geometry

Examples for these files are in the ./data folder

How to run:
1) Generate script: generateScriptsForAirwayAtlas.m
Input: (scriptsFile, dataFoldName, resultsDirName, sampleNum)
  -- scriptsFile: the name of the script file
  -- dataFoldName: the name of the folder where the data locate
  -- resultsDirName: the name of the folder where the results will be stored
  -- sampleNum: the sampling number of the cross sections 

P.S.: You can change the names for the input and output files.

Example: generateScriptsForAirwayAtlas( 'runTest', './data', './results', 100 );

2) chmod +x runTest

3) ./runTest

All the results will be generated in the folder './results'.